Agriculture Reference
In-Depth Information
This was a milestone, since these maps provided
inexpensive, PCR-based markers to then con-
struct or anchor new maps to perform QTL
analysis. Another milestone reached was the
development of the fi rst SSR-based consensus
map of wheat (Somers et al., 2004), which posi-
tioned >1,200 then-publicly available SSRs on a
single genetic map and facilitated new map con-
struction, chromosome anchoring, and compara-
tive mapping with SSRs.
mapping. Aside from the work at Institut für
Pfl anzengenetik und Kulturpfl anzenforschung
(IPK) by M. Roder and colleagues, the Wheat
Microsatellite Consortium (WMC), a public and
private effort with >30 members, developed >800
SSRs between 1997 and 2004. This set of WMC
microsatellites has been used worldwide along
with GWM and GDM SSRs to generate many
genetic maps of wheat (Chalmers et al., 2001;
Somers et al., 2004, 2006; McCartney et al., 2006).
More recently, the USDA developed and mapped
540 SSR markers labeled BARC (Beltsville Agri-
cultural Research Center) (Song et al., 2005), and
a joint venture between Genoplante and Institut
Scientifi que de Recherche Agronomique (INRA)
research center in Clermont Ferrand, France,
developed 252 SSRs labelled CFA, CFD,
and CFT (http://wheat.pw.usda.gov/GG2/index.
shtml).
In addition to SSR development, capillary
electrophoresis became available and affordable
for many institutes, which facilitated high-
throughput genotyping at low cost. The equip-
ment from Applied Biosystems Inc. (Foster City,
California), in particular, was well suited for SSR
detection and facilitates automated allele calling.
When SSRs are abundant and the use of a
high-throughput detection platform is available,
QTL analysis becomes much more feasible and
is only limited by the time to create popula-
tions and collect phenotypic data over several
environments.
Aside from searching for SSRs within genomic
DNA libraries and sequences, a bioinformatics
approach was developed to fi nd SSR sequences
within the growing public wheat database of
expressed sequence tags (ESTs) (Kantety et al.,
2002). This approach made sense since the cost
of sequencing had already been absorbed by the
EST sequencing efforts earlier, and only the cost
of primer synthesis and PCR would be required
to demonstrate the utility of these SSRs. This
idea was also attractive since it would provide
markers from within expressed genes, and gene
sequence conservation could facilitate cross-
species application or comparative mapping in
other cereal species (Sorrells et al., 2003; La Rota
and Sorrells 2004).
Consensus map
Since publication of the fi rst SSR-based genetic
map of wheat (Roder et al., 1998), other genetic
maps have been produced and the number of
SSRs has increased severalfold. Comparative
mapping between wheat genetic maps facilitated
more marker identifi cation in smaller regions of
the genome. This was done by lining up drawings
of maps and identifying markers in syntenic
regions on different maps (Fig. 14.1). In 2004, a
microsatellite consensus map was developed from
a union of four wheat genetic maps (Somers et al.,
2004), and this placed >1,200 loci onto a single
map of wheat. This single map is very useful for
anchoring new wheat genetic maps based on SSRs
and identifying multiple markers on chromosome
arms that may be deployed for MAS. For example,
the gene
Lr16
was mapped to the terminal end of
2BS (McCartney et al., 2005b), along with the
gene for Orange blossom wheat midge (
Sm1
)
(Thomas et al., 2005); SSRs in the region are
useful today for selection of lines for these pest
resistance traits.
Progress in marker technology
The largest advance in technology related to
genotyping and genetic mapping came with PCR-
based markers, and in particular SSRs. Develop-
ment of SSRs was proceeding in many crop
species through the use of genomic DNA libraries
enriched for short tandem repeats of DNA (mic-
rosatellites). The polyploid nature of wheat made
this particularly diffi cult, since genome-specifi c
markers are much more preferable for genetic
